Firstly, think about what Stephen does know.
Stephen says that God is evil because He allows suffering. See how he knows there is such a thing as evil. Notice how he is not a relativist - he is not saying that allowing evil would be something he would never do, but he can't force his morality onto others. Not a bit of it! He believes there is an objective standard and God has fallen short of it. He believes there are moral obligations and God has failed to meet them. But this is hopelessly confused and doomed to failure. What law is there above God? To what standard can He be held? The answer is none - morality can only flow from the nature of God.
If he could accuse God of being evil, and God were to say, "What do you mean by evil?" What would Stephen Fry say? Often when atheists are asked what they mean by evil they point to examples of it, but what they need to do (but can't) is give a definition - a definition that provides grounds for morality being objective and obligatory. Stephen Fry is saying that his morality is binding upon God, and the question is, who made Stephen Fry God so that he gets to dictate what God ought to do or allow?
If there are objective moral obligations then they cannot come from nature (why would they be obligatory?) They cannot come from society (that would mean no society could be called immoral!) They can only come from a righteous God. So Stephen Fry's moral outrage is proof that he is created in the image of a righteous God, and he knows it.
Secondly, think about what Stephen should know.
If all we had to go on was the current state of the world and there was nothing else to factor into the equation then we would perhaps be justified in feeling a little piqued with whoever was in charge, but we have more to go on...lots more to go on. There is an abundance of evidence for the truth of Christianity, and there is overwhelming proof (in the death of Christ) that God is a God of love and (in the resurrection of Christ) that God is a God of power.
Many millions across the world and throughout history can testify to the mighty moral transformation they experienced not through religion or church, but through believing the Gospel and trusting in Christ for salvation - their lives have been immediately, permanently, powerfully, positively changed, and so personal experience confirms what the evidence establishes, that God is good and powerful.
So even if we are at a complete loss to explain why God would allow suffering in this world, we have enough reason to trust Him - His love and power have been demonstrated and can be experienced.
Furthermore, Stephen acts as if no answer has ever been given to this question. He acts as if nothing took place in the past to explain suffering. The reason there is suffering in the world is because the head of God's creation fell into sin, and because the head fell the whole of creation fell too. We can't honestly or reasonably expect to live at a distance from God and yet have this world treat us as if there is no problem and everything is fine. The way this world is serves as a constant reminder that things are not the way they are supposed to be.
He acts as if nothing will take place in the future to eliminate suffering. When the Lord Jesus was here He performed miracles to authenticate His claim to be Messiah. These miracles showed what the world would be like when He reigns (they are called in Hebrews 6:5 the powers of the age to come). So what did He do? He healed the sick, raised the dead, calmed the storm, fed the hungry - all showing that suffering will be eliminated when He reigns. But He was rejected and so we continue to live in a world that hurts us. He offers us a place in that world to come, but only those who have repented can be there. For that reason it has not been ushered in as yet.
Again, he acts as if nothing happens in the present to encourage us in suffering. Stephen Fry does not know God and thus has no idea of the comfort He gives to His people. Those who are in a relationship with God can testify to the truth of Psalm 46:1, that God is a very present help in trouble.
Thirdly, think about what Stephen can't know.
The very first book written in the Bible (not Genesis, but Job) deals head on with people suffering through no fault of their own, and the teaching of the book is that God can't be accused of unrighteousness, because He is the Source and Standard of righteousness (e.g. Job 34:12-13; 36:22-23), and God knows far more than we do so it should be no surprise that we can't figure out why He allows everything He allows. This is not a cop out, because the fact is that the existence of God is indisputable - punting to atheism is not a reasonable option.
We recognise that we allow suffering, and even cause suffering, in the lives of our loved ones for reasons that we can't always explain to them. For example, vaccinating a child. The infant can have no idea why his mum allowed that to happen, and it would be futile for the mother to attempt to explain. In time, long after the pain has passed, the child will understand. In the meantime, the child knows the embrace and experiences the love of his mother. Surely even Stephen Fry would admit that if God exists then He is more knowledgeable than Stephen Fry is. He exhaustively knows the future and sees the full ramifications of every event. Stephen thinks he is pretty smart, but there's no way he would be able to process all the reasons even if God condescended to tell him. What we who are saved have is the evidence of His love and the experience of it, and that should be enough to go on until we reach heaven, and perhaps then, when all the sufferings of this life will seem like a pinprick, we will see the reason why. Here and now, we just can't know.
He says getting rid of God makes life more worth living. Try telling that to the parents who have lost a child or to someone afflicted by the awful suffering he speaks about. This is the ignorant, ivory tower, insulting nonsense these celebrity atheists come off with all the time. Multitudes who have known real suffering will tell Stephen Fry that in their deepest, darkest valleys, it was only the knowledge of God that made life worth living. What could Stephen Fry tell to the hopeless and the suffering that would make their life worth living? What comfort could he give to the bereaved, to the person who has just been given the dread diagnosis, etc. etc.? His talk is cheap, and his atheism makes everything ultimately worthless. God is the only reason life is worth anything.
Update, 10/2/15. A good friend gave me this point to finish with.
Finally, think about what Stephen will know.
He will stand before God and will know that God is right and he was wrong. Far better to agree with God now and receive His salvation and forgiveness, than agree with Him then when all that awaits us is the judgment we rightly deserve for our rebellion. Stephen Fry, and every one of us, needs the salvation that God has provided through Christ and offers in the Gospel. God offers it to him still, and to you as well.
